Multiple sequence alignment - TraesCS4B01G265600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G265600 chr4B 100.000 3209 0 0 1 3209 536917097 536920305 0.000000e+00 5927.0
1 TraesCS4B01G265600 chr4B 94.375 800 28 10 2419 3209 537153681 537154472 0.000000e+00 1212.0
2 TraesCS4B01G265600 chr4D 93.923 2896 125 32 332 3209 435649058 435651920 0.000000e+00 4325.0
3 TraesCS4B01G265600 chr4D 83.665 251 25 6 107 346 435648722 435648967 4.170000e-54 222.0
4 TraesCS4B01G265600 chr4A 92.403 2422 117 23 1 2393 37030300 37032683 0.000000e+00 3391.0
5 TraesCS4B01G265600 chr4A 92.788 832 36 14 2392 3209 37032738 37033559 0.000000e+00 1182.0
6 TraesCS4B01G265600 chr4A 95.082 61 0 2 2315 2374 37032684 37032742 3.410000e-15 93.5
7 TraesCS4B01G265600 chr2D 87.654 81 10 0 2011 2091 143757886 143757806 9.480000e-16 95.3
8 TraesCS4B01G265600 chr2B 87.654 81 10 0 2011 2091 201769433 201769353 9.480000e-16 95.3
9 TraesCS4B01G265600 chr2A 87.654 81 10 0 2011 2091 157547375 157547455 9.480000e-16 95.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G265600 chr4B 536917097 536920305 3208 False 5927.0 5927 100.000000 1 3209 1 chr4B.!!$F1 3208
1 TraesCS4B01G265600 chr4B 537153681 537154472 791 False 1212.0 1212 94.375000 2419 3209 1 chr4B.!!$F2 790
2 TraesCS4B01G265600 chr4D 435648722 435651920 3198 False 2273.5 4325 88.794000 107 3209 2 chr4D.!!$F1 3102
3 TraesCS4B01G265600 chr4A 37030300 37033559 3259 False 1555.5 3391 93.424333 1 3209 3 chr4A.!!$F1 3208

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
642 778 0.037605 ACCGAAGCTTCCGATTTCGT 60.038 50.0 20.62 6.19 41.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2358 0.319469 GCCTAGCTAGCAGCAGTAGC 60.319 60.0 18.83 6.9 45.56 3.58 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.838554 TAACAGCACCCCTACCTGCA 60.839 55.000 0.00 0.00 35.73 4.41
79 80 4.639310 CCTGTTAGCTCATGATGCTTCTTT 59.361 41.667 20.02 3.94 41.46 2.52
80 81 5.819379 CCTGTTAGCTCATGATGCTTCTTTA 59.181 40.000 20.02 4.42 41.46 1.85
81 82 6.018098 CCTGTTAGCTCATGATGCTTCTTTAG 60.018 42.308 20.02 13.04 41.46 1.85
82 83 6.409704 TGTTAGCTCATGATGCTTCTTTAGT 58.590 36.000 20.02 2.26 41.46 2.24
83 84 7.555965 TGTTAGCTCATGATGCTTCTTTAGTA 58.444 34.615 20.02 2.71 41.46 1.82
84 85 7.492669 TGTTAGCTCATGATGCTTCTTTAGTAC 59.507 37.037 20.02 9.62 41.46 2.73
85 86 6.232581 AGCTCATGATGCTTCTTTAGTACT 57.767 37.500 12.22 0.00 37.52 2.73
86 87 7.353414 AGCTCATGATGCTTCTTTAGTACTA 57.647 36.000 12.22 0.00 37.52 1.82
87 88 7.206687 AGCTCATGATGCTTCTTTAGTACTAC 58.793 38.462 12.22 0.00 37.52 2.73
88 89 7.069331 AGCTCATGATGCTTCTTTAGTACTACT 59.931 37.037 12.22 0.00 37.52 2.57
89 90 8.353684 GCTCATGATGCTTCTTTAGTACTACTA 58.646 37.037 0.91 0.00 0.00 1.82
90 91 9.672086 CTCATGATGCTTCTTTAGTACTACTAC 57.328 37.037 0.91 0.00 28.93 2.73
91 92 9.409918 TCATGATGCTTCTTTAGTACTACTACT 57.590 33.333 0.91 0.00 37.04 2.57
94 95 9.902684 TGATGCTTCTTTAGTACTACTACTACT 57.097 33.333 0.91 0.00 35.54 2.57
168 169 3.058160 CAGCCTGCCAAACCTCCG 61.058 66.667 0.00 0.00 0.00 4.63
179 180 3.767630 AACCTCCGCGCCTTGTGTT 62.768 57.895 0.00 0.00 0.00 3.32
184 194 0.317799 TCCGCGCCTTGTGTTAGTTA 59.682 50.000 0.00 0.00 0.00 2.24
185 195 0.719465 CCGCGCCTTGTGTTAGTTAG 59.281 55.000 0.00 0.00 0.00 2.34
207 217 2.887152 GTCTGTTCTTGATTTGGGCACT 59.113 45.455 0.00 0.00 0.00 4.40
238 255 2.282603 TTGTTTGGGCGGTAGGGC 60.283 61.111 0.00 0.00 41.35 5.19
241 258 2.044555 GTTTGGGCGGTAGGGCTTC 61.045 63.158 0.00 0.00 41.87 3.86
246 263 1.298667 GGCGGTAGGGCTTCTTTCA 59.701 57.895 0.00 0.00 38.40 2.69
247 264 0.322187 GGCGGTAGGGCTTCTTTCAA 60.322 55.000 0.00 0.00 38.40 2.69
269 286 1.322538 GGCTGGGGTTATTGGTGCTG 61.323 60.000 0.00 0.00 0.00 4.41
274 291 3.426615 TGGGGTTATTGGTGCTGTTTAG 58.573 45.455 0.00 0.00 0.00 1.85
282 299 4.978438 TTGGTGCTGTTTAGGGTTACTA 57.022 40.909 0.00 0.00 0.00 1.82
284 301 4.161876 TGGTGCTGTTTAGGGTTACTAGA 58.838 43.478 0.00 0.00 32.16 2.43
287 304 4.081586 GTGCTGTTTAGGGTTACTAGAGCT 60.082 45.833 0.00 0.00 34.14 4.09
288 305 5.126707 GTGCTGTTTAGGGTTACTAGAGCTA 59.873 44.000 0.00 0.00 34.14 3.32
289 306 5.897824 TGCTGTTTAGGGTTACTAGAGCTAT 59.102 40.000 0.00 0.00 34.14 2.97
290 307 7.014038 GTGCTGTTTAGGGTTACTAGAGCTATA 59.986 40.741 0.00 0.00 34.14 1.31
291 308 7.562454 TGCTGTTTAGGGTTACTAGAGCTATAA 59.438 37.037 0.00 0.00 34.14 0.98
299 318 8.973182 AGGGTTACTAGAGCTATAATAAGATGC 58.027 37.037 0.00 0.00 0.00 3.91
339 465 4.255126 GCTTGTGGCATTGCTGTG 57.745 55.556 8.82 0.00 41.35 3.66
341 467 0.665369 GCTTGTGGCATTGCTGTGTC 60.665 55.000 8.82 0.00 41.35 3.67
369 495 3.495193 CGCCTGAATCTCAACATTTGTG 58.505 45.455 0.00 0.00 0.00 3.33
408 538 1.102809 TGCACCACTGCTGTTCTTGG 61.103 55.000 0.00 0.00 44.57 3.61
412 542 1.102809 CCACTGCTGTTCTTGGTGCA 61.103 55.000 0.00 0.00 0.00 4.57
446 576 2.597117 ATTTGCGGTATGTGCTGCGC 62.597 55.000 6.19 6.19 43.32 6.09
452 583 0.734889 GGTATGTGCTGCGCAATCTT 59.265 50.000 20.70 6.11 41.47 2.40
498 629 2.607631 AATTTGTGCTTGCTGTGCTT 57.392 40.000 0.00 0.00 0.00 3.91
499 630 3.731652 AATTTGTGCTTGCTGTGCTTA 57.268 38.095 0.00 0.00 0.00 3.09
507 642 5.294306 TGTGCTTGCTGTGCTTATAATAGAC 59.706 40.000 0.00 0.00 0.00 2.59
518 653 6.924060 GTGCTTATAATAGACAGGTGAACGAT 59.076 38.462 0.00 0.00 0.00 3.73
519 654 7.438459 GTGCTTATAATAGACAGGTGAACGATT 59.562 37.037 0.00 0.00 0.00 3.34
620 756 2.193087 ATCCCAACGGTTTCCTCGGG 62.193 60.000 6.84 6.84 34.81 5.14
640 776 0.727398 CCACCGAAGCTTCCGATTTC 59.273 55.000 20.62 0.00 0.00 2.17
642 778 0.037605 ACCGAAGCTTCCGATTTCGT 60.038 50.000 20.62 6.19 41.39 3.85
643 779 0.645868 CCGAAGCTTCCGATTTCGTC 59.354 55.000 20.62 0.00 41.39 4.20
644 780 1.630148 CGAAGCTTCCGATTTCGTCT 58.370 50.000 20.62 0.00 38.96 4.18
669 807 6.493115 TGTTGGAGATATCTTTGAGCCAAAAA 59.507 34.615 19.25 11.28 35.89 1.94
676 814 7.667219 AGATATCTTTGAGCCAAAAACTCTTCA 59.333 33.333 0.00 0.00 32.75 3.02
877 1016 7.166142 GCTAATTATTACTGTCACTGTCTCGTC 59.834 40.741 0.00 0.00 0.00 4.20
1063 1206 9.890629 TGAACAACTATGCTATTACTCAAAGAT 57.109 29.630 0.00 0.00 0.00 2.40
1080 1223 4.521130 AAGATTCGACAACTCTGCTACA 57.479 40.909 0.00 0.00 0.00 2.74
1125 1268 3.392616 CCATAGGCTACCTGGACATCTTT 59.607 47.826 8.23 0.00 34.61 2.52
1167 1310 4.148079 TCCACAATGTTTGCATCTACCAA 58.852 39.130 0.00 0.00 33.50 3.67
1179 1322 2.922740 TCTACCAAAAGCAGGACGTT 57.077 45.000 0.00 0.00 0.00 3.99
1340 1483 1.153208 GGATGCTGAGCAGGGTGAG 60.153 63.158 14.36 0.00 43.65 3.51
1509 1652 1.102222 ATGTCGGTAGCTCTCCGGAC 61.102 60.000 23.63 19.97 46.82 4.79
1536 1679 5.438761 TCGAGATCTCATCGCTCAATAAA 57.561 39.130 22.31 0.00 39.98 1.40
1573 1716 1.885871 GACTGTGGAAATGGCAGCC 59.114 57.895 3.66 3.66 33.87 4.85
1671 1814 5.000012 AGTATTTCGAGATGGACTGTGAC 58.000 43.478 0.00 0.00 0.00 3.67
1680 1823 4.443857 GACTGTGACAGTGCAGCA 57.556 55.556 24.63 0.00 45.44 4.41
1740 1883 1.305718 GCCTGGTCCTGAGGTCTCT 60.306 63.158 0.00 0.00 32.60 3.10
1758 1901 4.098807 GTCTCTAAGATCACTCCCAAGGAC 59.901 50.000 0.00 0.00 0.00 3.85
1914 2057 1.569653 AGAGCCAGGGTGTTACTACC 58.430 55.000 0.00 0.00 40.10 3.18
1979 2122 1.748122 CCCAGCCTGCAGTGATCAC 60.748 63.158 18.47 18.47 0.00 3.06
2106 2249 0.454600 TGGATGTCGAGAACGGTAGC 59.545 55.000 0.00 0.00 40.21 3.58
2114 2257 3.073101 GAACGGTAGCCCCTCGGT 61.073 66.667 0.00 0.00 0.00 4.69
2139 2282 5.353400 TGATAACATCGACTCGAGTACAACT 59.647 40.000 20.09 4.47 39.91 3.16
2145 2288 3.811497 TCGACTCGAGTACAACTGAGAAA 59.189 43.478 20.09 0.00 31.97 2.52
2211 2354 4.564613 GGAAGCAGAGCCTTCTTCTAAGTT 60.565 45.833 11.92 0.00 40.76 2.66
2212 2355 3.936564 AGCAGAGCCTTCTTCTAAGTTG 58.063 45.455 0.00 0.00 0.00 3.16
2213 2356 2.418280 GCAGAGCCTTCTTCTAAGTTGC 59.582 50.000 0.00 0.00 0.00 4.17
2214 2357 3.867984 GCAGAGCCTTCTTCTAAGTTGCT 60.868 47.826 0.00 0.00 0.00 3.91
2215 2358 3.683822 CAGAGCCTTCTTCTAAGTTGCTG 59.316 47.826 7.68 0.00 0.00 4.41
2216 2359 2.418280 GAGCCTTCTTCTAAGTTGCTGC 59.582 50.000 0.00 0.00 0.00 5.25
2329 2475 8.736244 GGTGTTATGCTTAGTTAAAAAGATGGA 58.264 33.333 3.57 0.00 0.00 3.41
2393 2539 8.357402 TGTGTAACATAGTATACTACTGCATGG 58.643 37.037 14.82 2.41 45.67 3.66
2409 2611 6.653020 ACTGCATGGAAGTAACTTGATGATA 58.347 36.000 0.00 0.00 0.00 2.15
2410 2612 6.540189 ACTGCATGGAAGTAACTTGATGATAC 59.460 38.462 0.00 0.00 0.00 2.24
2411 2613 6.653020 TGCATGGAAGTAACTTGATGATACT 58.347 36.000 0.00 0.00 36.07 2.12
2412 2614 7.112122 TGCATGGAAGTAACTTGATGATACTT 58.888 34.615 0.00 1.57 43.77 2.24
2413 2615 7.611467 TGCATGGAAGTAACTTGATGATACTTT 59.389 33.333 0.00 0.00 42.02 2.66
2467 2673 7.935338 AGTGCTAAATGTGTGAAATTCTTTG 57.065 32.000 0.00 0.00 0.00 2.77
2509 2715 5.738619 TCAGCTTACACATCAGGAAACTA 57.261 39.130 0.00 0.00 40.21 2.24
2527 2734 6.801862 GGAAACTAGTGTCATTTGCACAATAC 59.198 38.462 15.07 0.00 39.17 1.89
2529 2738 7.510549 AACTAGTGTCATTTGCACAATACTT 57.489 32.000 0.00 0.00 39.17 2.24
2531 2740 8.615878 ACTAGTGTCATTTGCACAATACTTTA 57.384 30.769 0.00 0.00 39.17 1.85
2555 2769 2.559998 GTGGCACCAATTATTCCACG 57.440 50.000 6.29 0.00 37.96 4.94
2617 2831 1.599071 CGACCACTGCATAATCGCAAT 59.401 47.619 0.00 0.00 42.45 3.56
2626 2840 3.693578 TGCATAATCGCAATGAAACAGGA 59.306 39.130 0.00 0.00 39.45 3.86
2627 2841 4.157472 TGCATAATCGCAATGAAACAGGAA 59.843 37.500 0.00 0.00 39.45 3.36
2737 2954 1.487142 TCCTCAAACCCAGTTTCGACA 59.513 47.619 0.00 0.00 33.10 4.35
2801 3018 6.674694 ATGAAGTGCTGATCAACATAGAAC 57.325 37.500 1.44 0.00 0.00 3.01
2844 3063 7.890127 AGTTTTACATGATTCAAATCTCCCTCA 59.110 33.333 0.00 0.00 36.39 3.86
2888 3107 8.648698 TTCAGGGATCTAAAATCAACAATTCA 57.351 30.769 0.00 0.00 0.00 2.57
2889 3108 8.648698 TCAGGGATCTAAAATCAACAATTCAA 57.351 30.769 0.00 0.00 0.00 2.69
2890 3109 9.087871 TCAGGGATCTAAAATCAACAATTCAAA 57.912 29.630 0.00 0.00 0.00 2.69
2996 3215 0.390998 GCTTCTCAGCGCTCTCCTTT 60.391 55.000 7.13 0.00 35.91 3.11
3190 3409 2.092212 CACCATCTCTTATGGCCTTGGT 60.092 50.000 3.32 1.50 42.82 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.500783 ATTGCAGGTAGGGGTGCTGT 61.501 55.000 0.00 0.00 40.54 4.40
10 11 0.817654 GAAATTGCAGGTAGGGGTGC 59.182 55.000 0.00 0.00 40.29 5.01
13 14 0.751643 CCGGAAATTGCAGGTAGGGG 60.752 60.000 0.00 0.00 0.00 4.79
18 19 2.871096 TTAGACCGGAAATTGCAGGT 57.129 45.000 9.46 8.15 39.10 4.00
168 169 1.730612 GACCTAACTAACACAAGGCGC 59.269 52.381 0.00 0.00 31.98 6.53
169 170 2.993899 CAGACCTAACTAACACAAGGCG 59.006 50.000 0.00 0.00 31.98 5.52
171 172 5.855045 AGAACAGACCTAACTAACACAAGG 58.145 41.667 0.00 0.00 35.14 3.61
179 180 6.472887 CCCAAATCAAGAACAGACCTAACTA 58.527 40.000 0.00 0.00 0.00 2.24
184 194 2.158475 TGCCCAAATCAAGAACAGACCT 60.158 45.455 0.00 0.00 0.00 3.85
185 195 2.029918 GTGCCCAAATCAAGAACAGACC 60.030 50.000 0.00 0.00 0.00 3.85
207 217 3.556213 CCCAAACAAGTACGAGGTGATCA 60.556 47.826 0.00 0.00 0.00 2.92
238 255 1.260544 CCCCAGCCCTTTGAAAGAAG 58.739 55.000 6.49 0.00 0.00 2.85
241 258 2.302587 TAACCCCAGCCCTTTGAAAG 57.697 50.000 0.00 0.00 0.00 2.62
246 263 0.790339 ACCAATAACCCCAGCCCTTT 59.210 50.000 0.00 0.00 0.00 3.11
247 264 0.041090 CACCAATAACCCCAGCCCTT 59.959 55.000 0.00 0.00 0.00 3.95
274 291 8.198778 GGCATCTTATTATAGCTCTAGTAACCC 58.801 40.741 0.00 0.00 0.00 4.11
282 299 3.772025 AGCCGGCATCTTATTATAGCTCT 59.228 43.478 31.54 0.00 0.00 4.09
284 301 3.261897 ACAGCCGGCATCTTATTATAGCT 59.738 43.478 31.54 0.00 0.00 3.32
287 304 4.286032 AGGAACAGCCGGCATCTTATTATA 59.714 41.667 31.54 0.00 43.43 0.98
288 305 3.073062 AGGAACAGCCGGCATCTTATTAT 59.927 43.478 31.54 0.00 43.43 1.28
289 306 2.438021 AGGAACAGCCGGCATCTTATTA 59.562 45.455 31.54 0.00 43.43 0.98
290 307 1.212935 AGGAACAGCCGGCATCTTATT 59.787 47.619 31.54 12.79 43.43 1.40
291 308 0.839946 AGGAACAGCCGGCATCTTAT 59.160 50.000 31.54 8.15 43.43 1.73
335 461 0.108662 TCAGGCGCATACAGACACAG 60.109 55.000 10.83 0.00 0.00 3.66
339 465 2.131183 GAGATTCAGGCGCATACAGAC 58.869 52.381 10.83 0.00 0.00 3.51
341 467 2.229675 TGAGATTCAGGCGCATACAG 57.770 50.000 10.83 0.00 0.00 2.74
408 538 3.747099 ATATCACACGAAAAGCTGCAC 57.253 42.857 1.02 0.00 0.00 4.57
412 542 3.426159 CCGCAAATATCACACGAAAAGCT 60.426 43.478 0.00 0.00 0.00 3.74
446 576 3.469629 CACAGCGTGTAAACGAAGATTG 58.530 45.455 10.31 1.58 34.64 2.67
452 583 0.102663 TCACCACAGCGTGTAAACGA 59.897 50.000 10.31 0.00 35.18 3.85
489 620 5.128663 TCACCTGTCTATTATAAGCACAGCA 59.871 40.000 12.62 0.00 34.34 4.41
498 629 9.878667 TTTGAAATCGTTCACCTGTCTATTATA 57.121 29.630 0.00 0.00 43.52 0.98
499 630 8.665685 GTTTGAAATCGTTCACCTGTCTATTAT 58.334 33.333 0.00 0.00 43.52 1.28
507 642 2.916111 CGGTTTGAAATCGTTCACCTG 58.084 47.619 1.80 0.00 43.52 4.00
518 653 0.658897 GTTCAGTCCGCGGTTTGAAA 59.341 50.000 32.63 21.10 31.98 2.69
519 654 0.179067 AGTTCAGTCCGCGGTTTGAA 60.179 50.000 29.66 29.66 0.00 2.69
620 756 1.305930 AAATCGGAAGCTTCGGTGGC 61.306 55.000 27.25 10.94 0.00 5.01
626 762 2.338500 ACAGACGAAATCGGAAGCTTC 58.662 47.619 18.54 18.54 44.95 3.86
640 776 4.505922 GCTCAAAGATATCTCCAACAGACG 59.494 45.833 5.51 0.00 32.26 4.18
642 778 4.471025 TGGCTCAAAGATATCTCCAACAGA 59.529 41.667 5.51 0.00 34.78 3.41
643 779 4.774124 TGGCTCAAAGATATCTCCAACAG 58.226 43.478 5.51 0.00 0.00 3.16
644 780 4.842531 TGGCTCAAAGATATCTCCAACA 57.157 40.909 5.51 0.00 0.00 3.33
676 814 6.127196 GGTCAAGGAATTCAGACTCACTATCT 60.127 42.308 18.36 0.00 0.00 1.98
877 1016 2.613133 GCTGAAGCTAAGCAGAATGGAG 59.387 50.000 14.76 0.00 40.52 3.86
961 1104 4.036734 ACTGCAATTAACACACACAAGGAG 59.963 41.667 0.00 0.00 0.00 3.69
1080 1223 2.036414 TCTCTGCCGGCTGTCTCT 59.964 61.111 29.70 0.00 0.00 3.10
1167 1310 3.857010 GCTTTGCATAAACGTCCTGCTTT 60.857 43.478 15.22 0.00 36.84 3.51
1179 1322 2.086869 GTGAGGCTCAGCTTTGCATAA 58.913 47.619 19.38 0.00 0.00 1.90
1258 1401 0.518636 CGTAGACCCTCGTCGAACAA 59.481 55.000 0.00 0.00 44.28 2.83
1340 1483 3.393854 TGGTCCTCCAGGTAGTTCC 57.606 57.895 0.00 0.00 39.03 3.62
1467 1610 2.192861 CAGGGACAGGCGCACAAAA 61.193 57.895 10.83 0.00 0.00 2.44
1475 1618 1.471676 CGACATAAGACAGGGACAGGC 60.472 57.143 0.00 0.00 0.00 4.85
1509 1652 1.196581 AGCGATGAGATCTCGATGACG 59.803 52.381 17.76 16.95 38.38 4.35
1573 1716 3.808466 TTCGATCTCACAAGGATCCAG 57.192 47.619 15.82 8.68 37.02 3.86
1612 1755 3.996363 TCATTCTCGTTCACCATGTTCAG 59.004 43.478 0.00 0.00 0.00 3.02
1679 1822 0.879765 CTTGCAGGTCTCAGCCTTTG 59.120 55.000 0.00 0.00 36.58 2.77
1680 1823 0.475906 ACTTGCAGGTCTCAGCCTTT 59.524 50.000 0.00 0.00 36.58 3.11
1691 1834 1.200716 CATGCTGTGGTAACTTGCAGG 59.799 52.381 0.00 0.00 38.88 4.85
1740 1883 5.103043 AGGATAGTCCTTGGGAGTGATCTTA 60.103 44.000 4.34 0.00 46.91 2.10
1758 1901 1.482593 ACAGGGCTTTCGTCAGGATAG 59.517 52.381 0.00 0.00 0.00 2.08
1815 1958 2.180204 CGATTGCGTCATGGGGGAC 61.180 63.158 0.00 0.00 34.42 4.46
1979 2122 3.612247 CTGGGCTGGAGGTTCACGG 62.612 68.421 0.00 0.00 0.00 4.94
2106 2249 1.411246 TCGATGTTATCAACCGAGGGG 59.589 52.381 0.00 0.00 40.11 4.79
2114 2257 5.806366 TGTACTCGAGTCGATGTTATCAA 57.194 39.130 23.89 0.00 34.61 2.57
2139 2282 1.445410 CGATGGCGACGGTTTCTCA 60.445 57.895 0.00 0.00 40.82 3.27
2166 2309 2.255770 AGAAGACCCTAGGACCCTTG 57.744 55.000 11.48 0.00 0.00 3.61
2213 2356 1.000385 CCTAGCTAGCAGCAGTAGCAG 60.000 57.143 18.83 9.84 45.56 4.24
2214 2357 1.035923 CCTAGCTAGCAGCAGTAGCA 58.964 55.000 18.83 2.41 45.56 3.49
2215 2358 0.319469 GCCTAGCTAGCAGCAGTAGC 60.319 60.000 18.83 6.90 45.56 3.58
2216 2359 1.000385 CAGCCTAGCTAGCAGCAGTAG 60.000 57.143 18.83 9.14 45.56 2.57
2509 2715 8.575589 TCAATAAAGTATTGTGCAAATGACACT 58.424 29.630 7.64 0.00 44.49 3.55
2527 2734 6.980397 GGAATAATTGGTGCCACTCAATAAAG 59.020 38.462 10.59 0.00 33.72 1.85
2529 2738 5.954752 TGGAATAATTGGTGCCACTCAATAA 59.045 36.000 10.59 0.00 33.72 1.40
2531 2740 4.160252 GTGGAATAATTGGTGCCACTCAAT 59.840 41.667 13.12 5.92 44.23 2.57
2555 2769 6.862209 TGTAATTGGTGGCAAATCTAACATC 58.138 36.000 0.00 0.00 0.00 3.06
2634 2850 8.664669 TCCTGACATATATTTGCCATCTACTA 57.335 34.615 0.00 0.00 0.00 1.82
2636 2852 7.148340 GCTTCCTGACATATATTTGCCATCTAC 60.148 40.741 0.00 0.00 0.00 2.59
2823 3040 6.359804 CCTTGAGGGAGATTTGAATCATGTA 58.640 40.000 6.50 0.00 37.89 2.29
2844 3063 5.259632 CTGAAATCACTGAATTCTCCCCTT 58.740 41.667 7.05 0.00 0.00 3.95
2996 3215 3.857157 CCCCCGAATTCTCATAAGGAA 57.143 47.619 3.52 0.00 0.00 3.36


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.